# MAG-SOLex Molecular Representation: A Methodology for Handling Complex Molecules in Algorithms

## TL;DR

This paper introduces a new method for representing complex molecules using two matrices to capture detailed structural and chemical information efficiently.

## Contribution

The novel contribution is combining MAG and SOLex matrices to provide a detailed and versatile molecular representation for algorithmic use.

## Key findings

- The MAG matrix captures detailed bond information between atoms in a molecule.
- The SOLex matrix represents molecular cores with 44 increments in vectors for multicore structures.
- The combined methodology enables efficient calculation of thermodynamic properties and identification of reactive sites.

## Abstract

Different molecular representations exist to provide
visual and
mathematical means to depict complex structures. However, the detailing
required for algorithmic applications remains a challenge. This study
presents a methodology that uses two matrices to obtain a detailed
molecular description. The proposed matrices are Molecule as a Graph
(MAG), which describes a molecular graph providing detailed information
about the bonds between atoms in a molecule, and an extended version
of Structure-Oriented-Lumping (SOLex), representing each core in a
molecule with 44 increments organized into vectors, capable of describing
multicore structures. The combined use of these representations integrates
the agility of SOLex with the structural detailing of MAG, enabling
a rapid acquisition of detailed information about molecules. This
can be applied in the calculation of thermodynamic properties using
group contribution methods, as well as in the depiction of chemical
reactions at molecular level, enabling precise identification of groups
and reactive sites in molecules efficiently, even in complex algorithms.
The methodology was designed for hydrocarbons from petroleum and biomass-derived
sources, but can also be applied to different types of molecules,
providing a versatile and efficient means of handling molecular information.